| Understanding and engineering complex biomolecular networks in the cell are the goals of systems and synthetic biology. The effects of localization, spatial heterogeneity and molecular noise in biomolecular networks are not well understood. In this research, a theoretical approach to accurately simulate large biomolecular networks using the Monte Carlo method was introduced. Incorporating this theory, a computational tool named Monte Carlo Biomolecular Simulator (MBS) was developed, enabling studies of biomolecular kinetics with both spatial and temporal resolutions. The accuracy of MBS was verified by comparison against the classical deterministic approach. Furthermore, the effects of localization, spatial heterogeneity and molecular noise were studied in three simulated systems, showing their huge impact on the overall reaction kinetics. Lastly, the MBS was used as an engineering tool to create and fine-tune a synthetic protein network analogous to a D-latch memory unit commonly used in electrical circuits. |
